Fingolimod and natalizumab significantly reduce disease activity in relapsing-remitting multiple sclerosis (RRMS) and could promote tissue repair and neuroprotection. The ratio between conventional T1- and T2-weighted sequences(T1w/T2w-ratio) and magnetization transfer ratio (MTR) allow to quantify brain microstructural tissue abnormalities. Here, we compared fingolimod and natalizumab effects on brain T1w/T2w-ratio and MTR in RRMS over 2years of treatment. RRMS patients starting fingolimod (n = 25) or natalizumab (n = 30) underwent 3T brain MRI scans at baseline (T0), month 6 (M6), month 12 (M12), and month 24 (M24). White matter (WM) lesions, normal-appearing (NA) WM, and gray matter (GM) T1w/T2w-ratio and MTR were estimated and compared between groups using linear mixed models. No baseline demographic, clinical, and MRI difference was found between groups. In natalizumab patients, lesion T1w/T2w-ratio and MTR significantly increased at M6 vs. T0 (p ≤ 0.035) and decreased at subsequent timepoints (p ≤ 0.037). In fingolimod patients, lesion T1w/T2w-ratio increased at M12 vs. T0 (p = 0.010), while MTR gradually increased at subsequent timepoints vs. T0 (p ≤ 0.027). Natalizumab stabilized NAWM and GM T1w/T2w-ratio and MTR. In fingolimod patients, NAWM T1w/T2w-ratio and MTR significantly increased at M24 vs. M12 (p ≤ 0.001). A significant GM T1w/T2w-ratio decrease at M6 vs. T0 (p = 0.014) and increase at M24 vs. M6 (p = 0.008) occurred, whereas GM MTR was significantly higher at M24 vs. previous timepoints (p ≤ 0.017) with significant between-group differences (p ≤ 0.034). Natalizumab may promote an early recovery of lesional damage and prevent microstructural damage accumulation in NAWM and GM during the first 2years of treatment. Fingolimod enhances tissue damage recovery being visible after 6months in lesions and after 2years in NAWM and GM.